sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
1995-01-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.420 | 8.500 | 7.480 | 1.490 | 10.600 | 3 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_HUMAN |
| AC: | P00374 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.939 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.212 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 71.72 | 28.28 |
| According to VolSite | |
| HET Code: | MXA |
|---|---|
| Formula: | C17H19N5O2 |
| Molecular weight: | 325.365 g/mol |
| DrugBank ID: | DB03695 |
| Buried Surface Area: | 70.41 % |
| Polar Surface area: | 109.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 30.5037 | 14.661 | -1.05121 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| N4 | O | ILE- 7 | 2.97 | 175.13 | H-Bond (Ligand Donor) |
| C21 | CZ | PHE- 22 | 3.37 | 0 | Hydrophobic |
| C3' | CE2 | PHE- 22 | 3.12 | 0 | Hydrophobic |
| C6 | CZ | PHE- 22 | 3.28 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 30 | 3.47 | 123.1 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLU- 30 | 2.67 | 152.67 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 30 | 2.65 | 167.59 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 30 | 3.31 | 125.79 | H-Bond (Ligand Donor) |
| C4A | CB | PHE- 34 | 4.33 | 0 | Hydrophobic |
| C5M | CE1 | PHE- 34 | 3.92 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 34 | 4.4 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 34 | 3.91 | 0 | Aromatic Face/Face |
| DuAr | DuAr | PHE- 34 | 3.91 | 0 | Aromatic Face/Face |
| C5M | CG2 | THR- 56 | 4.47 | 0 | Hydrophobic |
| C21 | CB | SER- 59 | 4.08 | 0 | Hydrophobic |
| C2' | CG1 | ILE- 60 | 3.77 | 0 | Hydrophobic |
| C51 | CG | PRO- 61 | 3.49 | 0 | Hydrophobic |
| C4' | CG | PRO- 61 | 4.37 | 0 | Hydrophobic |
| N4 | O | VAL- 115 | 3.08 | 133.61 | H-Bond (Ligand Donor) |
| C5M | CB | VAL- 115 | 4.03 | 0 | Hydrophobic |
| C5M | C4N | NDP- 187 | 3.83 | 0 | Hydrophobic |
| C21 | C2D | NDP- 187 | 3.72 | 0 | Hydrophobic |
